Cell Fracture addon leaving unfractured boxes?
This is caused by a failed boolean operation.

The cell fracture uses the boolean modifier internally, if boolean fails because of geometry it can't handle (typically because of a non-manifold mesh), this happens.

Note that for 2.70 the boolean modifier has been upgraded to support ngons and a newer version of carve, so this will likely improve results in some cases, however there are limits to what boolean can operate on since it relies on calculating inside/outside of a mesh which can be problematic.